THE EVOLUTION LIST

THE EVOLUTION LIST is a forum for commentary, discussion, essays, news, and reviews that illuminate the theory of evolution and its implications in original and insightful ways. Unless otherwise noted, all materials may be quoted or re-published in full, with attribution to the author and THE EVOLUTION LIST. The views expressed herein do not necessarily reflect those of Cornell University, its administration, faculty, students, or staff.

Friday, January 24, 2014

Far Above Cayuga's Waters...

Another week of sub-zero weather here in Utopia, NY, and still Cayuga's waters (the ones we are far above) stubbornly remain waters, not ice. Yes, there's about 100 yards of crumbling rime ice drifted up against the shore at Stewart Park, but the rest of the lake is open water. COLD open water, but water nonetheless.

By contrast, when I first started teaching at Cornell (back in the Pleistocene, or the 1970s, I forget - it was so long ago), Cayuga's waters routinely froze over end-to-end, sometimes so thick that a truck could drive across it. Indeed, back in the late 1800s, there was a thriving winter industry in Ithaca, whereby guys in heavy clothing would drive teams of horses and wagons out onto the ice, which they cut with big saws into two-foot-thick blocks and shipped to New York City in boxcars full of sawdust, to supply the ice boxes and ice houses of the Big Apple. Even as late as the 1980s, hardy Ithaca folk would drag their ice fishing shacks (some were more like mini-resorts) out onto the ice, where they would remain until just before breakup in March.

But now, despite two bone-chilling "polar vortices" (which are genuine meteorological phenomena, despite the rantings of Rush Windbag), Cayuga's waters remain...water. Why? Could it be that a few decades of increased atmospheric heat has warmed those billions of gallons of lake water to the point that a few days of sub-zero cold won't freeze them any more? And could this foreshadow what will happen as the immensely larger oceans of the world absorb more and more heat from the warming atmosphere? And could that have something to do with the fact (and yes, it is a FACT) that the atmosphere hasn't had this much carbon dioxide in it since the Jurassic? And could that be due to the fact that since the 1800s we have released an almost incomprehensible quantity of carbon dioxide into the atmosphere, while cutting down millions of acres of forest that used to take it up and turn it into wood? Damn good question...

And an even better question: if this keeps up, what will the world be like in a few more decades, much less a few more centuries?

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As always, comments, criticisms, and suggestions are warmly welcomed!
--Allen

Monday, November 04, 2013

Myths in Biology: Mendel's Pea Flowers

At P.Z. Myers' blog, Pharyngula, he has a post on the subject of "myths" in biology, using the number of cell types in humans as an example. He cites Stephen J. Gould's famous article on fox terriers as an example of such myths and how they get incorporated in the science of biology.

You want myths in biology? Pick up any introductory biology textbook and look up Mendel’s original experiments with garden pea plants. Look at the color illustration of the seven phenotypic characters Mendel supposedly tested. Is purple versus white flower color in the figure? Now, read Mendel’s paper describing the seven different characters in garden peas that he studied (you can find the original paper here, in the original German and in English translation). Is purple versus white flower color in the list of characters tested? Interesting…

Toward the end of the paper, Mendel mentions that in a later set of experiments he tested flower color and found the same ratios that he found with the original seven traits he tested. According to the paper, he tested “violett-rothe und weiss Blüthenfarbe” (i.e. “violet-red and white blossom color”), but this test was NOT in his original set of seven experiments, which are the ones always illustrated in biology textbooks.

So, when did biology textbooks start this particular myth? As far as I can tell it was in the first biology textbook with full color illustrations: William T. Keeton’s Biological Science, 2nd ed. The illustrator thought he could kill two birds with one stone by illustrating the technique used to ensure controlled fertilization (i.e. removing the stamens from the flowers using iris scissors) and purple and white flower color. Except that Mendel didn’t study purple versus white flower color in his original series of seven crosses.

Which pair of traits did Mendel actually study, but were replaced by purple versus white flowers in all introductory biology textbooks? The color of the seed-coat, in which gray-brown is dominant and white is recessive. According to Mendel’s original paper, gray-brown seed coats are associated with (what we would now refer to as linked with) “violet-red blossoms and reddish spots in the leaf axils,” but once again Mendel did NOT explicitly test purple versus white flower color in the experiments for which he is remembered, and for which the science of “Mendelian genetics” is named.

And why is the clearly incorrect list (and colored figure) of the seven traits Mendel supposedly studied included in every introductory biology textbook today? Because Keeton’s textbook was the most widely used textbook in biology for decades, so all of the other publishers simply copied what was in his textbook as a way of gaining market share.

Can this myth be corrected now? How many professors’ sets of lecture notes and PowerPoint slides would have to be changed to correct this mistake, and how many textbooks would need new illustrations that included the correct list of the seven traits, and how many people would complain about these changes, or (even worse) suggest that Mendel really did study purple and white flower color in his original series of seven experiments?

Sunday, March 31, 2013

Why vaccinate your children?

QUESTION: Not immunizing does not expose someone to a disease, only actual exposure to the disease does so. If a vaccine is effective and your children are vaccinated, how does an unvaccinated person put them at risk? Especially if that person has not been exposed to the disease in question?

ANSWER: It has to do with herd immunity (also known as "community immunity"). With the exception of the smallpox vaccination (reaction to which is easily observed), none of the vaccinations we give our children are tested individually to see if they "took". This is difficult at best and next to impossible in many cases. Instead, the effectiveness of a vaccination program is measured by the prevalence of the disease before, during, and after vaccination of a target population. If the prevalence of the disease goes down as more people are vaccinated (this is verified using statistical analysis), then the vaccination is assumed to work even if it doesn't in some cases.

In fact, no vaccination (including the smallpox vaccination) works in every single case. There is a small, but non-zero fraction of any vaccinated population in which the vaccination doesn't "take" (this again is statistically testable). What this means is that in any population that has been vaccinated, there is a small residual fraction that is still susceptible to the infection.

The rate at which an infection is transmitted depends upon the "infection triangle": (1) virulence (how easily the infectious agent enters a potential host), (2) resistance (how easily the host fights off the infection), and (3) prevalence (how many carriers/potential spreaders there are in the population). Herd immunity depends on 2 and 3, and is defined as that percentage of a vaccinated population that is high enough to stop further transmission of the infection. For example, epidemiologists (doctors who study how infectious diseases spread through populations) define the "herd immunity threshold" for diptheria as 85% (see here). This means that in a population in which at least 85% of the individuals have been vaccinated against diptheria, the probability of an infectious individual spreading the disease to an unprotected member of the population (i.e. the 15% who have not been vaccinated or in whom the vaccination hasn't "taken") is sufficiently low that unprotected individuals probably won't be exposed.

The problem here is that "unprotected" doesn't necessarily mean "unvaccinated". Like any real process in the real world, not all vaccinations "take". A small but non-zero fraction of vaccinations don't cause the vaccinated individual to develop permanent resistance to the disease. This can happen from a number of factors, including the immune status of the vaccinated individual and variations in the potency of the vaccine. This means that, like the actual rate of resistance following vaccination, the probability that a vaccinated individual is actually resistant to the infection is not 100%, but usually somewhere between 80% and 95%. What this means is that the actual level of herd immunity is lower than the rate of vaccination, sometimes by quite a bit (this is a function of both individual variations and group variability - some people are more likely to develop resistance than others).

Therefore, if people in a population don't get vaccinated, then the size of the susceptible carrier population is larger, and if it's large enough (i.e. greater than the "herd immunity threshold"), then the probability that the infectious agent will be spread is high enough that susceptible individuals (i.e. those that have not been vaccinated AND those whose vaccinations didn't "take") will be exposed to the infectious agent, get the disease, and spread it to other susceptible individuals.

This is why there have recently been mini-epidemics of pertussis (whooping cough), measles, and other infectious diseases that were formally almost completely eliminated. Badly educated people (including, but not limited to people who have a visceral anti-science/anti-government bias) don't vaccinated their children, who become part of the susceptible population who, if they are numerous enough, can spread the disease to others, including those whose vaccinations didn't "take".

So, how do you know if your vaccination (or your kid's vaccination) "took" or not? Simple answer: you don't (indeed, in most cases, even with the old smallpox vaccination, you can't). Therefore those of us who don't want our children sickened, crippled, or killed by a preventable infectious disease are counting on everyone else getting their children vaccinated to the point at which the "herd immunity" of our community is above the "transmissibility threshold" and therefore won't be exposed to the infectious agent.

The same kind of reasoning that underlies the concept of "herd immunity" can be used to see if the argument that increased vaccinations cause autism is valid. If there is a causative relationship between increased vaccinations and autism, and if the underlying causative agent is thimerosol in the vaccinations, then there should be a decrease in autism since thimerosol was removed from the vaccinations. No such correlation has been found; ergo, thimerosol in vaccinations was not the causative agent for the perceived increase in frequency of autism.

Another potential test of this hypothesis is to see if those children who, for whatever reason (e.g. immune dysfunctions, religious prohibitions, lack of access to vaccines, etc.) have NOT been vaccinated have lower rates of autism. This is also not the case, so once again the hypothesis that vaccinations (and specifically vaccinations with serum that has been preserved with thimerosol) cause autism is unfounded. This is precisely the kind of statistical correlation testing that is the basis for every single one of the peer-reviewed epidemiological studies that have been done to determine if there is a causative link between vaccinations and autism (or ADHD, or your choice of mental disorder for which we do not yet know the underlying cause). And every single one of these studies (and there have now been many, including several meta-analyses of multiple studies) have shown no statistically significant (i.e. real) correlation between rates of vaccination and the observed rate of increase in autism, ADHD, and some other developmental disorders?.

So, what is causing the statistically detectable increase in the rate of autism, ADHD, and some other developmental disorders? There are plenty of candidates. People (both men and women) are having children at older ages, which has been shown to be causally related to some of these disorders. People are exposed to increasing levels of artificial chemicals and heavy metals in the environment, which again have been shown to be causally related to some of these disorders. Perhaps most significantly, the diagnostic criteria for some of these disorders have changed, especially for ADHD and autism, which are now considered to be "spectrum" disorders, rather than single pathologies that one either has or does not have. Had the current criteria for these developmental disorders been used when I was a kid, I would almost certainly have been diagnosed with ADHD and also probably mild Aspergers' syndrome (i.e. autism spectrum disorder). When you change the definition of a disease, you change your perception of its prevalence.

The same is not the case for the demonstrated decline in crippling and potentially fatal diseases, however. There is very strong statistical evidence that this dramatic decline over the past century and a half has been due to two factors: vaccination and public health. Both of these were and are developed by medical scientists, implemented by health professionals, and supported (and in some cases legally mandated) by governments, usually at the state level.

I believe that it is the case that in New York State you can refuse to have your children vaccinated for religious reasons, yet the public schools are still required to let those children attend classes and therefore expose all of their classmates to an increased possibility of contracting a potentially crippling or fatal disease. In my opinion this is wrong: children who have not been vaccinated should not be allowed to even enter a public building, much less attend public school. Sure, their parents can exercise their right to endanger their children's health (whether their children have a right to not be endangered by their parents is another question), but that right should not take precedence over the rights of other parents (and their children) to not be exposed to the threat of contracting the diseases that such parents have exposed their children to.

Friday, February 01, 2013

The Evolution of Cooperation – Three Theories or One (or None)?

Ever since Darwin, evolutionary biologists have thought and written (and argued about) the evolution of cooperation. In the 20th century, at least three different major theories were proposed to explain how cooperation (and especially unselfish altruism) could evolve by natural selection. Several attempts to unify these theories have been made and are currently a topic of intense debate.

Now, as part of Cornell's Darwin Days celebration, you are invited to come to a dinner discussion to hear about, think about, talk about, and (hopefully) argue about these theories and their implications for human behavior, ethics, and philosophy.

PRESENTER: Allen MacNeill, Senior Lecturer in Biology and Evolution at Cornell and author of Evolutionary Biology and Evolutionary Psychology

SPONSORS: Liebermania! and the Cornell Human Ethology Forum (this will also be the organizational meeting for CHEF)

DAY, TIME, & LOCATION: Thursday 14 February 2013 at 6:00 PM at Risley Dining/Tammany at Cornell University. This event is part of Cornell and PRI/MOTE's Darwin Day 2013 celebration.

Please contact Allen MacNeill at adm6@cornell.edu by Tuesday 12 February 2013 if you plan to attend this event. Hope to see you there!

Saturday, September 10, 2011

There's a new poll out on the percentage of Americans who agree with the scientific evidence in favor of the theory of evolution. The new poll was conducted by Anderson Robbins Research and Shaw & Company Research for Fox News (polling data are here). The questions asked in the poll are very similar to those in the periodic polls on this question conducted by the Gallup organization (their polling data are here).

As a professional evolutionary biologist and someone who has followed this debate for decades, I find the Fox News poll results surprisingly encouraging. Although the fraction of the American public that agrees with the Young Earth Creationist position hasn't changed significantly for almost half a century, the fraction that agrees with the position taken by evolutionary biologists has increased very significantly since the Gallup organization first polled Americans on this question in 1982.

Here are the data, in chronological order:

Percent of Americans agreeing with evolutionary theory:

GALLUP:1982 9%1994 11%2002 12%2006 14%

FOX NEWS:2011 21%

From 9% to 21% in only twenty-nine years (i.e. less than two generations)! If you plot the data, the increase is clearly exponential, with the inflection point at around 2006 (i.e. following the Kitzmiller-Dover decision). At the current exponential rate of increase, the "evolutionary biology" position should be the majority position within another generation. This is why we need to keep presenting the science, and why creationists (including the "intelligent design" variety) are their own worst enemies.

Wednesday, June 08, 2011

Teleological Explanations in Biology

Biologists tend to use teleological language in explaining the origin and evolution of living organisms and their characteristics. As John Reiss has pointed out (Reis, J. Not by Design: Retiring Darwin's Watchmaker, University of California Press, 2009), this entails the idea that evolution is necessarily a teleological process. This entails the idea that evolution is not a "natural" process, like gravity or oxidation, and that therefore there is some "non-natural" component (i.e. "magic") in biology that fundamentally distinguishes it from the other natural sciences.

Evolutionary biologists like Richard Dawkins try to make this distinction when referring to the problem of human free will (see "Let's all stop beating Basil's car"), but unless they are careful about how they talk about evolution (especially natural selection) they revert to the same teleological descriptions and explanations that Reiss so decries. What is the problem, here?

• Variety: structural and functional differences between individuals in populations,

• Heredity : the inheritance of structures and functions from parents to offspring (either genetically or epigenetically),

• Fecundity : the ability to reproduce, especially (but not necessarily) at a rate that exceeds replacement, and

• Demography : some individuals survive and reproduce more often than others.

As a result of these four processes, the heritable characteristics of some individuals become more common in populations over time.

Notice that the same list of processes can be used to explain non-adaptive evolutionary change (e.g. genetic drift). Also notice that the only source of new phenotypic variations is what I have called the "engines of variation": all of those processes that produce heritable phenotypic changes in phylogenetic lines of organisms in populations. There are at least fifty such processes (you can see a summary list here). While it is the case that "random mutation" is included in this list, there are many other processes in this list that do not involve "mutation" (in the genetic sense) and which also are not "random" (at least insofar as that term is often used).

Is there a real distinction between non-teleological and teleological processes, or are all processes either teleological or not? If all processes (i.e. changes over time) are teleological, as asserted by Aristotle (and some of the commentators), then there is no point in talking about it. However, if some processes are teleological and some are not (as most people, including presumably most of the commentators here, now believe), then the question becomes "how can one distinguish between teleological and non-teleological processes, and what explains the differences between them?"

In his comprehensive analysis of teleology, Andrew Woodfield (Woodfield, A. Teleology, Cambridge University Press, 1976) pointed out that all teleological descriptions can be reformulated to conform to the linguistic formula " x happens in order to/for y outcome." He also asserted that such linguistic formulations describe metaphysically real processes. That is, some processes are genuinely teleological – they involve pre-existing designs or plans that cause processes to tend toward particular outcomes, regardless of perturbations or outside interference – while other processes only seem teleological – they involve laws of nature, such as gravity, that result in particular outcomes, without responding actively to perturbations or outside interference.

This distinction is essential when considering whether "genuine" teleology exists. To be precise, teleological descriptions sound "reasonable" when they are applied to genuinely teleological processes, but sound ridiculous if they are applied to non-teleological processes. For example, does it sound reasonable to say that when you drop a rock, it falls "in order to" reach the ground? By contrast, does it sound reasonable to say that birds have wings "in order to" fly? Is there a difference between the "reasonableness" of the first teleological explanation and the second?

When I pose this question to my students, almost all of them say yes: the first is ridiculous and the second isn't. I then point out that this implies that the origin of the wings of birds therefore seems to be the result of a teleological process. I then point out (reprising Aristotle) that there are at least four ways of explaining the presence of wings: • "this bird has wings because it is composed of materials that are assembled and operated as wings" (Aristotle's "material" cause);• "this bird has wings because its parents had wings" (Aristotle's "efficient" cause);• "this bird has wings because birds have wings" (Aristotle's "formal" cause); and • "this bird has wings in order to fly" (Aristotle's "final" cause).

To say that natural selection is teleological would therefore require that there be a pre-existing encoded program somewhere that would cause natural selection to bring about its effects. This is ridiculous for at least two reasons:• there is no such program as far as we can tell (where would it be encoded?), and• this would require that natural selection be a process in and of itself, rather than the outcome of the four processes listed above.

Sunday, May 29, 2011

The Metaphysical Foundations of Modern Science

I started attending the weekly meetings of the Ithaca Friends Meeting in September, 1969. One of the people who made an immediate and lasting impression on me was an older gentlemen, always impeccably dressed, who sometimes spoke in meeting in a quavery, but very determined voice. His "messages" were always very literate, but not necessarily complicated. I was eventually introduced to him, and learned that his name was "Ned" Burtt, and that he was one of the founders of the Ithaca meeting.

After several years we became good friends, but only in the context of the Friends Meeting. I got to know his wife, Marjory, with whom I had many very engaging conversations. She was a retired psychotherapist with an interest in Eastern philosophy, especially Buddhism. I didn't have as many conversations with Ned, not because he wasn't willing, but because he was almost completely deaf. Indeed, after a few years I noticed that Marjory and some of his older friends took turns sitting next to him in meeting, and when someone rose to speak, would write down what they said on a slip of paper and pass it to Ned.

Year later I was co-teaching a course on the history and philosophy of science, for which the teaching staff had chosen as one of the required readings a "classic" in the history of science, The Metaphysical Foundations of Modern Science, by Professor Edwin Arthur Burtt, the Susan Lynn Sage Professor of Philosophy at Cornell University. Translated into dozens of languages and continuously in print since 1924, Burtt's Metaphysical Foundations was often mentioned as the precursor to Thomas Kuhn's The Structure of Scientific Revolutions, and one of the seminal texts in the history of science.

Imagine my surprise (and chagrin) when I discovered that "Ned" Burtt of the Ithaca Friends Meeting was Prof. Edwin Arthur Burtt himself, author of the Metaphysical Foundations and perhaps the most famous historian of science in the first half of the 20th century. Characteristically, he never mentioned it in any of our conversations (brief and halting as they were), and no one else in meeting seemed to think it important enough to mention either.

Ned died in 1989 at the age of 97, and was memorialized at the Ithaca Meeting in our usual way – a silent meeting, punctuated by a few heart-felt "messages" from his friends. I think of him now as I am re-reading once again his Metaphysical Foundations, and am once again struck by his keen insight and masterful use of language. Here's just one sample:

"The glorious romantic universe of Dante and Milton, that set no bounds to the imagination of man as it played over space and time, had now been swept away. Space was identified with the realm of geometry, time with the continuity of number. The world that people had thought themselves living in – a world rich with colour and sound, redolent with fragrance, filled with gladness, love and beauty, speaking everywhere of purposive harmony and creative ideals – was crowded now into minute corners in the brains of scattered organic beings. The really important world outside was a world hard, cold, colourless, silent, and dead, a world of quantity, a world of mathematically computable motions in mechanical regularity. The word of qualities as immediately perceived by man became just a curious and quaint minor effect of that infinite machine beyond. In Newton the Cartesian metaphysics, ambiguously interpreted and stripped of its distinctive claim for serious philosophical consideration, finally overthrew Aristotelianism and became the predominant world-view of modern times.

*Whew* - talk about a splash of cold water in the face. It is this world-view – the one that forms the basis of all of modern science, including biology – that depresses and terrifies those who cannot live without the "old magic" and motivates those who want to tear down "modern" science and go back to the pre-scientific world-view, what Carl Sagan called "the demon-haunted world." But, just like the magic realm of childhood, there is no going back now, not to the innocent and often terrifying universe of the childhood of our cultures. In the words of Bertrand Russell (one of Ned Burtt's contemporaries):

"That Man is the product of causes which had no prevision of the end they were achieving; that his origin, his growth, his hopes and fears, his loves and beliefs, are the outcome of accidental collections of atoms...that all the labours of the ages, all the devotion, all the inspiration, all the noonday brightness of human genius, are destined to extinction in the vast death of the solar system, and that the whole temple of Man's achievement must inevitably be buried beneath the debris of a universe in ruins...only on the firm foundation of unyielding despair can the soul's habitation henceforth be safely built." – A Free Man's Worship [1923]

And so tomorrow (it's Memorial Day once again), I will go walking through the little grave yard out behind the Hector Meeting House where Ned and Marjory are buried, and think once again about the old, deaf gentleman whose messages were so eloquent and whose view of reality so unflinching.

Thursday, March 17, 2011

Evolutionary Psychology: The Science of Human Nature

Having been tickled by Google Alert that my name had been mentioned in the comments at Pharyngula (P. Z. Myer's blog), I took a quick look. Just a few comments for now:

1) I became an evolutionary psychologist when studying the behavioral ecology of Microtus pennsylvanicus got boring. Those cute little field voles got boring because their ethology is relatively simple. Human ethology is a lot more interesting, mostly because it is a lot more complex. Should we not try to study it because it is more complex? Or because it might not jibe with some people's political preconceptions?

An evolutionary adaptation is any heritable phenotypic character whose frequency of appearance in a population is the result of increased reproductive success relative to alternative versions of that heritable phenotypic character.

4) Here are the criteria I believe are most useful when one is attempting to determine if one is dealing with an "adaptation":

Qualification 1: An evolutionary adaptation will be expressed by most of the members of a given population, in a pattern that approximates a normal distribution;

Qualification 2: An evolutionary adaptation can be correlated with underlying anatomical and physiological structures, which constitute the efficient (or proximate) cause of the evolution of the adaptation;

Qualification 3: An evolutionary adaptation can be correlated with a pre-existing evolutionary environment of adaptation (EEA), the circumstances of which can then be correlated with differential survival and reproduction; and

Qualification 4: An evolutionary adaptation can be correlated with the presence and expression of an underlying gene or gene complex, which directly or indirectly causes and influences the expression of the phenotypic trait that constitutes the adaptation.

To me, it seems reasonable that if one can apply those to a specific human behavior, one can make arguments about its evolutionary derivation. Would anyone disagree?

As for the ridiculous idea that evolutionary psychology only deals with sex, has anyone making such a claim actually read a textbook on the subject? Here are several:

If you haven't, then please do so, and then we can discuss these questions.

While we're on the subject, Part II of Evolutionary Psychology: The Science of Human Nature (on the ethology of between-group behavior in humans) is coming out in May. My next project is an introductory textbook in evolutionary biology, entitled Evolutionary Biology: The Darwinian Revolutions, again in two parts. Part I (due out in September) is The Modern Synthesis and Part II (due out next May) is The Evolving Synthesis.

After that (if I live that long) will be On Purpose: The Evolution of Design by Means of Natural Selection (won't there be some fireworks when that comes out?), in which I present one of the core arguments for The Metaphysical Foundations of the Biological Sciences, in the spirit of E. A. Burtt's The Metaphysical Foundations of Modern Physical Science. Should be fun!

Thursday, December 09, 2010

Is Science True?

In my experience, everyone bases their "arguments on certain metaphysical suppositions, scientists and non-scientists included. As a good friend and student of E. A. Burtt, I have found his Metaphysical Foundations of Modern Physical Science to be extraordinarily useful in this regard. In fact, I have begun work on what I hope will be a companion volume: Metaphysical Foundations of Modern Biological Science, in which I will examine the assumptions that underlie the science of biology as it is practiced today.

One of the bedrock assumptions underlying both modern physics and modern biology is non-teleology: the assumption that natural processes do not include any teleological input. I personally think that this is wrong, and base my objection to this idea on Ernst Mayr's monumental book, Toward a New Philosophy of Biology, published in 1988. Mayr argued very persuasively that teleological explanations are entirely appropriate in biology insofar as they refer to the development and maintenance of living organisms. According to Mayr, both of these processes (and indeed all biological processes) are directed by programs (i.e. genomes, etc.) that pre-exist the entities and processes that they specify and regulate. In the jargon of the current debate, genomes and other developmental programs are "designs" for the assembly and operation of living organisms.

However, Mayr also argued very strongly that the origin of biological programs – that is, the various mechanisms of biological evolution – need not (and apparently do not) include any teleological component. Like all physical processes, there is no detectable "grand design" (much less a Grand Designer) which/Who has formulated beforehand the programs that regulate life. In other words, teleology is entirely appropriate when applied to life and the operation of living programs, but not when applied to the origin of life or the origin of living programs.

So, what does this say about the question of whose opinions to trust when considering these issues? My first criterion is skepticism: if someone claims to know the truth about anything at all (including, of course, the contents of their own mind), my immediate reaction is intense skepticism. Science (at least that version of it that has been practiced since the 17th century) isn't about truth. It's about reasonable confidence in explanatory models, all of which are grounded on a metaphysical assumption of the usefulness of methodological naturalism. Notice I wrote "usefulness", not "truth", because as far as I can tell the only "truth" that exists on either side of the evolution/ID divide is a version of Colbert's "truthiness". It feels like "truth", but isn't really. In my opinion, "experts" are people who keep these distinctions in mind at all times, and do not easily (if ever) use absolute statements when talking about nature.

For example, I have an immediate, knee-jerk negative reaction to the title of Jerry Coyne's book, Why Evolution is True, and indeed to much of what he writes for the general public. Consider a similar title, Why Quantum Mechanics is True, or if you prefer Why the Gas Laws are True. How would a physicist react to titles such as these? I hope (and my general experience has been) that they would object to the word "true", and also perhaps to the question "why". Physics isn't about "truth" and doesn't usually ask about "why" things happen. Physics is about "useful" and "consistent" and "empirically testable" models of reality, and it's about "how" things happen, not "why" they happen.

Indeed, in the natural sciences (including biology) the answer to the question "how" is the same as the answer to the question "why". How do birds come to have wings? They inherit a genetic and developmental program that, via interactions with their environment, produces those structures we call "wings". Why do birds come to have wings? Same answer. How have birds acquired these genetic and developmental programs? They evolved by natural selection and other evolutionary mechanisms. Why have birds acquired these genetic and developmental programs? Again, same answer.

Speculating as to whether the biological processes by which the programs that specify and regulate living organisms and processes are somehow externally/supernaturally directed seems to me to be metaphysical arguments, rather than scientific ones. Interesting, compelling even, but not part of science, at least as it has been practiced for a very long time.

Saturday, December 04, 2010

Many Metabolisms, Many Origins?

An unspoken but widely held belief among both evolutionary biologists (and some "intelligent design" supporters) is the idea that life (or, to be more specific, living organisms and/or metabolic processes) originated once a very long time ago. Along with my fellow biology majors, I was taught this by William T. Keeton in introductory biology at Cornell, where we also were told that if life (or biomolecules) somehow spontaneously started again today, it would immediately be scarfed up by already living organisms.

"There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." [Origin of Species, 1st edition, 1859]

Darwin asserted this partly to contrast his theory of evolution from that of Lamarck's, which included the idea that life was continuously arising spontaneously, generating new phylogenetic lines of organisms throughout deep evolutionary time. The discovery of the (almost) "universal" genetic code in the 1950s by Crick, Nirenberg, Holley, Khorana, et al provided strong evidence for the "one origin" hypothesis.

However, the fact that there is currently no evidence for an alternative "many origins" hypothesis doesn't necessarily support the conclusion that this hypothesis has been falsified. On the contrary, as the recent discovery by Felisa Wolfe-Simon of a "shadow arsenic metabolism" indicates, this lack of evidence is the result of lack of investigation, rather than actual lack of such origins. It is, in other words, quite possible that life (or at least biochemical processes similar to metabolic processes and molecules similar to "standard" biomolecules, and even cell-like structures incorporating both) is "originating" spontaneously all the time, but that we haven't noticed it because we haven't been looking. After all, nobody suspected the existence of an entire domain of living organisms (i.e. the Archaea) until Carl Woese starting looking two decades ago.

As J. B. S. Haldane — who formulated an early hypothesis for the origin of life — once quipped,

"[T]he Universe is not only queerer than we suppose, but queerer than we can suppose." [Haldane, J. B. S. (1927) Possible Worlds and Other Papers, page 227]

Wednesday, November 10, 2010

What is "Darwinism" and am I a "Darwinist"?

I don’t use the term “Darwinism” at all, any more than I would use the term “Newtonism” when referring to classical physical mechanics, “Einsteinism” to refer to relativity theory, “Bohr/Feinman/Heisenberg/Schroedingerism” to refer to quantum mechanics, or “Mendeleevianism” to refer to chemistry. What I and my colleagues (and friends) do is probably best described as “evolutionary biology”, and includes (at a bare minimum) the following:

1) the formulation and testing of a set of interconnected theories explaining the origin of biological diversity, consisting of descent with modification from common ancestors over deep geological time, describable via cladistic analysis, and supported by inference from multiple sources of empirical evidence, including comparative anatomy, biogeography, developmental biology, genomics, historical geology, and paleontology; and

2) the formulation and testing of a separate but related set of interconnected theories explaining the origin and modification of the phenotypic characteristics of living organisms, consisting (at a bare minumum) of the mechanisms of natural selection, sexual selection, genetic drift, and neutral molecular evolution in deep geological time, grounded (at least in part) in theoretical mathematical models of population genetics, depending on multiple sources of heritable phenotypic variation, and supported by inference from multiple sources of empirical evidence, including field and laboratory research in the fields of biochemistry, cell biology, comparative physiology, developmental biology, ecology, ethology, genetics, neurobiology, and physiological ecology.

Note that these two definitions of the principle domains of evolutionary biology correspond roughly to what are sometimes referred to as “macroevolutionary theory” and “microevolutionary theory” (in that order) and do not explicitly mention:

• theories of the origin of life from non-living materials, which are properly the purview of astrophysics, chemistry, and geology, not biology;

• the concept of “adaptation”, which has had a checkered past in evolutionary biology and is facing increasing challenges within the field; and

• teleology, which is almost never mentioned, except for those evolutionary biologists who have thought about it (which, in my experience, are relatively few), who generally assume that resort to teleological explanations in evolutionary biology is unnecessary. Not wrong, just unnecessary (not to mention unproductive as an empirical research hypothesis).

As philosophical concepts, both adaptation and teleology have a very long history, stretching back at least to Plato and Aristotle. However, recent developments in evolutionary theory, including (but not limited to) theories of epigenetics, exaptation, genetic drift/draft, neutral and nearly neutral molecular “drift” in deep evolutionary time, and punctuated equilibrium, have rendered the concept of “adaptation” as an increasingly marginal diversion rather than a central topic in evolutionary biology.

And teleology, rather than being considered “wrong” (when it is considered at all, which is seldom) is now increasingly being incorporated into new theories of “evolved agency”, especially in evolutionary psychology (my own field). I am currently working on a treatise on this latter subject, which I hope to finish before departing this veil of tears and laughter for that undiscovered country from whose bourn no traveller returns.

Sunday, June 06, 2010

The Annotated Origin of Species

In November of 1859, the London publishing house of John Murray brought out the first edition of what would become the most famous and important work of science of the 19th century: Charles Darwin'sOn the Origin of Species. The first edition of 1,250 copies sold out in one afternoon (first edition copies today fetch over a hundred thousand dollars on the rare book market) and was eventually reprinted over the next fifteen years in five increasingly popular editions. The success of the Origin catapulted Darwin from a relatively unknown specialist in the taxonomy of barnacles to the most famous naturalist of the 19th century and became the most widely read (and most controversial) science text of all time.

Many historians of biology credit the Origin with founding the modern science of biology. Hence, it is very curious that the first edition of the Origin lacks what most scholars expect to find in such influential and widely respected works. Unlike most other books of its kind — including Darwin's other famous books, The Voyage of the Beagle (first published in 1839) and The Descent of Man (first published in 1871) — the Origin has virtually none of the usual "machinery" of a scholarly work. Although Darwin cites the findings and opinions of hundreds of naturalists worldwide in the Origin, he does not provide any footnotes or written citations to their published works. The first edition of the Origin also does not include a bibliography nor any listing of published references. And, despite focusing on the most visual of the natural sciences, the Origin contains only one illustration, a hand–drawn diagram of the branching pattern of descent that Darwin proposed for his theory of descent with modification (his term for what we now refer to as "evolution").

The reason for this surprising lack of documentation is well known: Darwin had been scooped on his theory of natural selection by a fellow English naturalist, Alfred Russel Wallace. In April of 1858, Wallace sent Darwin a letter that included a brief essay "On the Tendency for Varieties to Depart Indefinitely from the Original Type", in which Wallace anticipated virtually all of the major concepts of Darwin's theory of evolution by natural selection. Darwin had been working on his theory for over two decades, and had been writing the book that would eventually be published as the Origin for at least five years when he received Wallace's letter. Anxious to preserve his priority as the discoverer of natural selection and urged on to do so by his friends and fellow naturalists, Darwin rushed what he considered to be an "abstract" of his ideas into print in November of 1859. This "brief abstract", published without footnotes, illustrations, or bibliography, was the first edition of the Origin of Species by Means of Natural Selection.

The first edition of the Origin was a masterwork and is still published in its original form, without footnotes, illustrations, and bibliography. Reading it, one can still get a taste of the overwhelming scholarship with which Darwin supported what he called his "long argument" for descent with modification. However, to really appreciate how much of the science of natural history Darwin wove into his argument, one really needs to know what Darwin's sources were and how they were related to each other.

Presenting these sources and showing how Darwin marshaled them in his defense of his theory is the heart of James Costa's brilliant annotation of Darwin's classic, The Annotated Origin, published by Belknap Press of Harvard University Press. Brought out in celebration of the 150th anniversary of the publication of first edition of the Origin, Costa's annotated version more than compensates for the "missing" material in Darwin's original. The introduction to The Annotated Origin alone is worth the price of the book. In it, Costa presents a lightning biography of Darwin and a nuanced exploration of the reasons for his rush to publish in 1859. It also contains a reader's guide to the Origin, a book that is often difficult for modern readers who are unaccustomed to the density of Victorian prose. Costa then analyzes and annotates virtually every page of the Origin, including the title page, in which he provides a brief history of Darwin's illustrious publisher, John Murray, and his decision to print only 1,250 copies of what would eventually become his best-selling and most famous publication.

Costa's annotations run the gamut from personal anecdotes to hard-science references. He weaves together Darwin's own telegraphic notes in his unpublished notebooks, his correspondence, his other published works, and his autobiography, providing the reader with a wealth of information and insight. Tracking down each line of evidence becomes a kind of "exploration" in itself. One can follow threads of evidence that elucidate Darwin's views about nature, science, his fellow naturalists, and even such "taboo" subjects (at least in the Victorian era) as sex and the intimate details of family life.

Costa's annotations also provide a detailed framework for Darwin's argument, showing how the various explanations and examples are marshaled in such a way as to support Darwin's underlying argument for "descent with modification by means of natural selection." As just one example, consider Costa's annotations to the section of pigeon breeding in the first chapter of the Origin ("Variation Under Domestication"). Naïve readers of this chapter are sometimes puzzled by Darwin's emphasis on pigeon breeding and its relationship to his theory. But, as Costa points out, "[p]igeons provided a microcosm of Darwin's model of selection, as well as valuable data on development, correlation of traits, and reversion." Like so many of his Victorian contemporaries, Darwin raised pigeons at his country estate at Down House in Kent, and conducted dozens of breeding experiments to test his theories. Darwin pointed out that all of the various breeds of pigeons could be shown to have descended from the wild rock pigeon (Columba livia) by a process that we now refer to as artificial selection. Darwin constructed an argument by analogy that natural selection followed the same rules as artificial selection. And, since so many of his contemporaries (and potential readers) were also pigeon fanciers, he could be reasonably confident that they would be able to follow his argument without extensive explanation or citations of obscure references to the scientific literature.

Reading the first edition of Darwin's Origin of Species is a revelation. One catches the threads of Darwin's argument and follows his reasoning through to his startling (and sometimes troubling) conclusions. James Costa's masterful annotation of the Origin does much more. It supplies the scholarly apparatus that the first edition lacked and provides a coherent and comprehensive background for Darwin's arguments, as well as many fascinating insights into Darwin's personality, thought processes and research methods. No other scientist has been as exhaustively analyzed as Darwin, and no other published work of science has been as widely criticized or praised as the Origin of Species. Reading James Costa's Annotated Origin provides an even deeper appreciation for Darwin's achievement and its impact on science and society.